biostudies-literatureAnandakrishnan MNIH HHSNIGMS NIH HHSvbaf289https://www.ebi.ac.uk/biostudies/studies/S-EPMC12664573biostudies-literatureUnknown5(1)<h4>Motivation</h4>Protein kinases regulate cellular signaling pathways through a cascade of phosphorylation activity, selectively targeting specific residues on substrate proteins (phosphosites). Determining the characteristics of kinases that phosphorylate specific substrates have been extensively studied. Most tools utilize amino acid sequence motifs around phosphosites but don't consider substrate protein's biological characteristics.<h4>Results</h4>We present KSMoFinder, a kinase-substrate-motif prediction model that learns factors beyond motif similarities by integrating proteins' biological contexts. We learn the semantics in a knowledge graph containing proteins' contextual relationships, kinase-specific motifs and motif composition, and represent the proteins and motifs as vectorsBioinformatics advancesKSMoFinder-knowledge graph embedding of proteins and motifs for predicting kinases of human phosphosites.PMC12664573R35 GM141873U24 OD038424Anandakrishnan MWu CHChen CVijay-Shanker KRoss KEfalseKSMoFinder-knowledge graph embedding of proteins and motifs for predicting kinases of human phosphosites.<h4>Motivation</h4>Protein kinases regulate cellular signaling pathways through a cascade of phosphorylation activity, selectively targeting specific residues on substrate proteins (phosphosites). Determining the characteristics of kinases that phosphorylate specific substrates have been extensively studied. Most tools utilize amino acid sequence motifs around phosphosites but don't consider substrate protein's biological characteristics.<h4>Results</h4>We present KSMoFinder, a kinase-substrate-motif prediction model that learns factors beyond motif similarities by integrating proteins' biological contexts. We learn the semantics in a knowledge graph containing proteins' contextual relationships, kinase-specific motifs and motif composition, and represent the proteins and motifs as vectors2025-01-01T00:00:00Z20252026-05-23T03:26:00.813Z2026-05-23T03:13:56.933ZS-EPMC126645734132364810.1093/bioadv/vbaf289